Buggy code:
public class Main { public static void main ( String [ ] args ) throws IOException { boolean listClasses = false ; String ellaSettingsFile = null ; Config config = Config . g ( ) ; int i = 0 ; while ( i < ( args . length ) ) { String a = args [ i ] ; if ( a . equals ( "-l" ) ) { listClasses = true ; } else if ( a . equals ( "-x" ) ) { config . excludeFile = args [ ( i + 1 ) ] ; i ++ ; } else if ( a . equals ( "-ella.dir" ) ) { config . ellaDir = args [ ( i + 1 ) ] ; i ++ ; } else if ( a . equals ( "-ella.runtime" ) ) { config . ellaRuntime = args [ ( i + 1 ) ] ; i ++ ; } else if ( a . equals ( "-ella.settings" ) ) { ellaSettingsFile = args [ ( i + 1 ) ] ; i ++ ; } else if ( a . equals ( "-ella.apktool" ) ) { config . apktoolJar = args [ ( i + 1 ) ] ; i ++ ; } else if ( ( config . inputFile ) == null ) config . inputFile = a ; else { assert ( config . outputFile ) == null ; config . outputFile = a ; } i ++ ; } config . load ( ellaSettingsFile ) ; if ( ( config . inputFile ) == null ) { System . out . println ( "New<seq2seq4repair_space>input<seq2seq4repair_space>file<seq2seq4repair_space>to<seq2seq4repair_space>process" ) ; return ; } File inputFile = new File ( config . inputFile ) ; if ( ! ( inputFile . exists ( ) ) ) { System . out . println ( ( ( "Input<seq2seq4repair_space>file<seq2seq4repair_space>" + ( config . inputFile ) ) + "<seq2seq4repair_space>does<seq2seq4repair_space>not<seq2seq4repair_space>exist." ) ) ; return ; } String appPath = inputFile . getCanonicalPath ( ) ; config . appId = Util . appPathToAppId ( appPath ) ; App app = App . readApp ( config . inputFile , config . outDir ( ) , config . apktoolJar ) ; if ( listClasses ) { app . listClasses ( ) ; return ; } if ( ( config . outputFile ) == null ) { config . outputFile = ( ( config . outDir ( ) ) + ( File . separator ) ) + "instrumented.apk" ; } File updatedManifestFile = Main . updateManifest ( app . manifestFile ( ) ) ; File unsignedOutputFile = File . createTempFile ( "ellainstrumented" , ".apk" ) ; app . updateApk ( Instrument . instrument ( app . dexFilePath ( ) ) , updatedManifestFile , unsignedOutputFile , config . apktoolJar ) ; if ( config . outputFile . endsWith ( ".apk" ) ) <START_BUG> app . signAndAlignApk ( unsignedOutputFile , config . outputFile , config . keyStore , config . storePass , config . keyPass , config . alias ) ; <END_BUG> CoverageId . g ( ) . dump ( ) ; System . out . println ( "\n********************************************************************************" ) ; System . out . println ( "Install<seq2seq4repair_space>the<seq2seq4repair_space>following<seq2seq4repair_space>instrumented<seq2seq4repair_space>apk<seq2seq4repair_space>and<seq2seq4repair_space>then<seq2seq4repair_space>execute<seq2seq4repair_space>the<seq2seq4repair_space>app" ) ; System . out . println ( config . outputFile ) ; System . out . println ( "********************************************************************************\n" ) ; System . out . println ( "\n********************************************************************************" ) ; System . out . println ( "After<seq2seq4repair_space>coverage<seq2seq4repair_space>data<seq2seq4repair_space>is<seq2seq4repair_space>collected,<seq2seq4repair_space>view<seq2seq4repair_space>the<seq2seq4repair_space>coverage<seq2seq4repair_space>report<seq2seq4repair_space>at<seq2seq4repair_space>the<seq2seq4repair_space>following<seq2seq4repair_space>URL." ) ; System . out . println ( ( ( ( config . tomcatUrl ) + "//viewcoverage?apppath=" ) + appPath ) ) ; System . out . println ( "********************************************************************************\n" ) ; } static File updateManifest ( File manifestFile ) { } }

Fix:
app . signAndAlignApk ( unsignedOutputFile , config . outputFile , config . keyStore , config . storePass , config . keyPass , config . alias , config . zipAlign ) ;